Koichi Momma

Three-dimensional Visualization in Powder Diffraction

A multi-purpose pattern-fitting system, RIETAN-2000, has been extensively utilized to contribute to many structural studies. It offers a sophisticated structure-refinement technique of whole-pattern fitting based on the maximum-entropy method (MEM) in combination with a MEM analysis program PRIMA. We have recently completed a successor system, RIETAN-FP, to RIETAN-2000, adding new features such as standardization of crystal-structure data, an extended March-Dollase preferred-orientation function, and automation of imposing restraints on bond lengths and angles. Further, we have been developing a new three-dimensional visualization system, VESTA, using wxWidgets as a C++ application framework. VESTA excels in visualization, rendering, and manipulation of crystal structures and electron/nuclear densities determined by X-ray/ neutron diffraction and electronic-structure calculations. VESTA also enables us to display wave functions and electrostatic potentials calculated with part of these programs.

Dysnomia, a computer program for maximum-entropy method (MEM) analysis and its performance in the MEM-based pattern fitting

A computer program, Dysnomia, for the maximum-entropy method (MEM) has been tested for the evaluation and advancement of MEM-based pattern fitting (MPF). Dysnomia is a successor to PRIMA, which was the only program integrated with RIETAN-FP for MPF. Two types of MEM algorithms, i.e., 0th-order single-pixel approximation and a variant of the Cambridge algorithm, were implemented in Dysnomia in combination with a linear combination of the “generalized F constraints” and arbitrary weighting factors for them. Dysnomia excels PRIMA in computation speed, memory efficiency, and scalability owing to parallel processing and automatic switching of discrete Fourier transform and fast Fourier transform depending on sizes of grids and observed reflections. These features of Dysnomia were evaluated for MPF analyses from X-ray powder diffraction data of three different types of compounds: taurine, Cu 2 CO 3 (OH) 2 (malachite), and Sr 9 In(PO 4 ) 7 . Reliability indices in MPF analyses proved to have been improved by using multiple F constraints and weighting factors based on lattice-plane spacings, d , in comparison with those obtained with PRIMA.

Synthesis and crystal structure of a layered silicate HUS-1 with a halved sodalite-cage topology.

A new layered silicate, HUS-1, was synthesized by hydrothermal synthesis using decomposed FAU- and *BEA-type zeolites as nanosized silica parts. Structural analyses by X-ray powder diffractometry and solid-state magic-angle-spinning (MAS) NMR spectroscopy revealed that HUS-1 has a layered structure containing a silicate layer per unit cell along a stacking direction. Its framework topology is similar to that of SOD-type zeolites and consists of a halved sodalite cage, which includes four- and six-membered Si rings. Structure refinement by the Rietveld method showed that tetramethylammonium (TMA) ions used as a structure-directing agent (SDA) were incorporated into the interlayer. The four methyl groups of the TMA molecule were located orderly in a hemispherical cage in the silicate layer, which suggests restraint of molecular motion. The interlayer distance is estimated at about 0.15 nm, which is unusually short in comparison with that in other layered silicates (e.g., β-HLS or RUB-15) with similar framework topologies. The presence of hydrogen bonding between adjacent terminal O atoms was clearly revealed by the (1)H MAS NMR spectroscopy and by electron-density distribution obtained by the maximum entropy method.

Encapsulation kinetics and dynamics of carbon monoxide in clathrate hydrate.

Carbon monoxide clathrate hydrate is a potentially important constituent in the solar system. In contrast to the well-established relation between the size of gaseous molecule and hydrate structure, previous work showed that carbon monoxide molecules preferentially form structure-I rather than structure-II gas hydrate. Resolving this discrepancy is fundamentally important to understanding clathrate formation, structure stabilization and the role the dipole moment/molecular polarizability plays in these processes. Here we report the synthesis of structure-II carbon monoxide hydrate under moderate high-pressure/low-temperature conditions. We demonstrate that the relative stability between structure-I and structure-II hydrates is primarily determined by kinetically controlled cage filling and associated binding energies. Within hexakaidecahedral cage, molecular dynamic simulations of density distributions reveal eight low-energy wells forming a cubic geometry in favour of the occupancy of carbon monoxide molecules, suggesting that the carbon monoxide–water and carbon monoxide–carbon monoxide interactions with adjacent cages provide a significant source of stability for the structure-II clathrate framework.

Crystal structures of high-pressure phases in the alumina-water system: II. Powder X-ray diffraction study of a new dense aluminum deuteroxide, δ-Al(OD)3

In this study we report the solution of the structure of δ-Al(OD)3. The crystal structure was determined using powder X-ray diffraction and direct methods, while the positions of deuterium atoms were estimated by difference-Fourier methods and MEM/Rietveld analysis. In the A-site deficient hydroxy-perovskite-type structure of δ-Al(OD)3, we find two types of one-dimensional H-bonding network.

Computational simulations of the structure of Japan twin boundaries in quartz

The structures of Japan twin boundaries in quartz are studied through molecular dynamics simulations and energy minimization calculations. Four types of twinning are grouped under the Japan twin law, comprising 10 subtypes of geometrical configurations based on the structural handedness and composition plane. For each subtype, the twin displacement vector is determined and the structures of the twin boundaries with {11 22} or {TT22} composition plane are simulated. It is shown that six subtypes composed of two crystals with same-handed structure have the same type of SiO 4 tetrahedral linkage at twin boundaries. The twin boundary structures of these six subtypes can be further divided into two enantiomorphic structures composed of right- or left-handed quartz. The other four subtypes are composed of combinations of right- and left-handed quartz, and are structurally distinct from the same-handed group. The twin boundary energies of the same-handed group are lower than for the opposite-handed group. The Si-O bond lengths in the region of the twin boundary differ by no more than 0.05 A from those in the bulk quartz for all subtypes. The differences between the Si-O-Si angles at the twin boundaries and in the bulk exceed 20°, whereas the differences in O-Si-O angles are less than 10°. The present calculations demonstrate that SiO 4 tetrahedra at Japan twin boundaries are very stiff in comparison with inter-tetrahedral forces, consistent with previous reports for silica polymorphs, and that structural matching of twin individuals is primarily achieved through the rotation of SiO 4 tetrahedra.

Imayoshiite, Ca3Al(CO3)[B(OH)4](OH)6·12H2O, a new mineral of the ettringite group from Ise City, Mie Prefecture, Japan

Abstract Imayoshiite, Ca3Al(CO3)[B(OH)4](OH)6 ·12H2O, occurs in cavities in the altered gabbro xenolith in the sepentinized dunite exposed at Suisho-dani, Ise City, Mie Prefecture, Japan. Imayoshiite is colourless and transparent with a vitreous lustre and its aggregates are white with a silky lustre. Imayoshiite has a white streak. Its Mohs hardness is 2-3. It is brittle, the cleavage is distinct on {100} and the fracture is uneven. The mineral is uniaxial (-) with the indices of refraction ω = 1.497(2) and ε = 1.470(2) in white light. Imayoshiite is hexagonal, P63, a = 11.0264(11), c = 10.6052(16) Å by powder diffraction and a = 11.04592(2), c = 10.61502(19) Å by single-crystal diffraction. The structural refinement converged to R1 = 2.35%. Imayoshiite is the first member of the ettringite group with both CO3 and B(OH)4 anions.

MAGNDATA: towards a database of magnetic structures. I. The commensurate case

A free web page under the name MAGNDATA, which provides detailed quantitative information on more than 400 published magnetic structures, has been made available at the Bilbao Crystallographic Server (http://www.cryst.ehu.es). It includes both commensurate and incommensurate structures. In the first article in this series, the information available on commensurate magnetic structures was presented [Gallego, Perez-Mato, Elcoro, Tasci, Hanson, Momma, Aroyo & Madariaga (2016). J. Appl. Cryst. 49, 1750–1776]. In this second article, the subset of the database devoted to incommensurate magnetic structures is discussed. These structures are described using magnetic superspace groups, i.e. a direct extension of the non-magnetic superspace groups, which is the standard approach in the description of aperiodic crystals. The use of magnetic superspace symmetry ensures a robust and unambiguous description of both atomic positions and magnetic moments within a common unique formalism. The point-group symmetry of each structure is derived from its magnetic superspace group, and any macroscopic tensor property of interest governed by this point-group symmetry can be retrieved through direct links to other programs of the Bilbao Crystallographic Server. The fact that incommensurate magnetic structures are often reported with ambiguous or incomplete information has made it impossible to include in this collection a good number of the published structures which were initially considered. However, as a proof of concept, the published data of about 30 structures have been re-interpreted and transformed, and together with ten structures where the superspace formalism was directly employed, they form this section of MAGNDATA. The relevant symmetry of most of the structures could be identified with an epikernel or isotropy subgroup of one irreducible representation of the space group of the parent phase, but in some cases several irreducible representations are active. Any entry of the collection can be visualized using the online tools available on the Bilbao server or can be retrieved as a magCIF file, a file format under development by the International Union of Crystallography. These CIF-like files are supported by visualization programs like Jmol and by analysis programs like JANA and ISODISTORT.

Shimazakiite-4M and shimazakiite-4O, Ca2B2O5, two polytypes of a new mineral from Fuka, Okayama Prefecture, Japan

Abstract Shimazakiite occurs as greyish white aggregates up to 3 mm in diameter. Two polytypes, shimazakiite- 4M and shimazakiite-4O, have been identified, the former in nanometre-sized twin lamellae and the latter in micrometre-sized lamellae. Shimazakiite was discovered in an irregular vein in crystalline limestone near gehlenite-spurrite skarns at Fuka mine, Okayama Prefecture, Japan. Associated minerals include takedaite, sibirskite, olshanskyite, parasibirskite, nifontovite, calcite and an uncharacterized hydrous calcium borate. The mineral is biaxial (-), with the following refractive indices (at 589 nm): α = 1.586(2), β = 1.650(2), γ = 1.667(2) and 2Vcalc = 53º [shimazakiite-4M]; and α = 1.584(2), β = 1.648(2), γ = 1.670(2) and 2Vcalc = 54.88º [shimazakiite-4O]. Quantitative electronmicroprobe analyses (means of 28 and 25 determinations) gave the empirical formulae Ca2B1.92O4.76(OH)0.24 and Ca2B1.92O4.76(OH)0.24 for shimazakiite-4M and shimazakiite-4O, respectively. The crystal structure refinements: P21/c, a = 3.5485(12), b = 6.352(2), c = 19.254(6) Å , β = 92.393(13)º, V = 433.6(3) Å3 [for shimazakiite-4M]; and P212121, a = 3.55645(8), b = 6.35194(15), c = 19.2534(5) Å , V = 434.941(18) Å3[for shimazakiite-4O], converged into R1 indices of 0.1273 and 0.0142, respectively. The crystal structure of shimazakiite consists of a layer containing B2O5 units (two near-coplanar triangular corner-sharing BO3 groups) and 6- and 7-coordinate Ca atoms. Different sequences in the c direction of four layers are observed in the polytypes. The five strongest lines in the powder-diffraction pattern [listed as d in Å (I)(hkl)] are: 3.02(84)(022); 2.92(100)(104̅) 2.81(56)(104); 2.76(32)(113); 1.880(32)(118̅,126̅,126,118) [for shimazakiite-4M]; and 3.84(33)(014); 3.02(42)(022); 2.86(100)(104); 2.79(29)(113); 1.903(44)(126,118) [for shimazakiite-4O].

Minohlite, a new copper-zinc sulfate mineral from Minoh, Osaka, Japan

Abstract Minohlite, a new copper-zinc sulfate mineral related to schulenbergite, was found in the oxidized zone of the Hirao mine at Minoh (Minoo) City, Osaka Prefecture, Japan. The mineral occurs in cracks in altered shale as rosette aggregates up to 100 m m in diameter, composed of hexagonal platy crystals up to 50 μm m in diameter and 10μm m in thickness. The associated minerals are chamosite, muscovite, smithsonite, serpierite, ramsbeckite, ‘limonite’ and chalcopyrite. Minohlite has hexagonal (or trigonal) symmetry with unit-cell parameters of a = 8.2535(11), c = 8.1352(17) Å, V = 479.93(16) Å3 and Z = 1, and possible space groups P6, P6̅, P6/m, P622, P6mm, P6̅2m and P6/mmm (or P3, P3̅, P321, P3m1, P3̅m1, P312, P31m and P3̅1m). The six strongest reflections in the powder X-ray diffraction pattern [d in Å (I) hkl] are 8.138 (20) 001; 4.128 (24) 110; 2.702 (100) 120; 2.564 (76) 121; 1.560 (43) 140; and 1.532 (24) 141. Electron microprobe analyses gave the following values (wt.%): CuO 37.18, ZnO 21.08, FeO 0.49, SO3 16.78, SiO2 0.44, and H2O 24.03 (by difference). The empirical formula, calculated on the basis of Cu + Zn + Fe + S + Si = 9 atoms per formula unit, is (Cu4.43Zn2.45Fe0.06)Σ6.94[(SO4)1.99(SiO4)0.07]Σ2.06(OH)9.64·7.81H2O, which leads a simplified formula of (Cu,Zn)7(SO4)2(OH)10·8H2O where Cu > Zn. The mineral is bluish-green and transparent with a pearly to vitreous lustre. The streak is pale green. Cleavage is perfect on {001}. The Mohs hardness number is less than 2. The calculated density is 3.28 g cm−3. The mineral is named after Minoh City, where it was discovered.